Custom camera settings allow me to select, for example, a red filter (as I only work in B&W this is an advantage), is there any advantage to using this digital in-camera filter over a real red lens filter when it comes to final B&W image quality?

3 Answers
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In general not really. The are potentially some benefits e.g. a blue filter might prevent you from blowing the red channel and getting flare or other problems with excessive light (e.g. sensor bloom) if for some reason you have far more red light.

But generally using a coloured filter will just prevent you from changing your mind later compared to using the in-camera filter (and shooting raw) which to me is a massive disadvantage.

Better now :) Still, you wouldn't use strong color filter to correct lightning, you should use the weaker color correction filters instead. See also this answer: photo.stackexchange.com/questions/586/…
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KarelSep 27 '10 at 7:57

To my best knowledge, using strong color filters (like 25A, 38A, 99) on digital cameras have only downsides:

You're can very easily blow the channel which color the filter is (red channel if you use red filter)

You're underexposing other channels resulting more noise in these channels

The result is that you're only using efficiently 25% of your sensor (I don't know exactly how the Bayer works, but considering it's interpolating 66% of the image even without filters, one can imagine how poorly it does when it only has 1 correctly exposed channel available)

You're losing 1-2 (or even more depending on the filter) stops of exposure

The resulting photo is only usable for specific purposes

Having to actually buy the filter and screw it on

Considering there is no way to avoid Bayer interpolation and all the possibilities that open when doing the BW conversion in post, I'd suggest not to use these filters on digital cameras. So shoot RAW and add the effects you want afterwards.

Here are some examples. Both images were shot RAW, developed using Monochrome Picture Style in DPP with exactly the same settings, shot with red filter had its brightness adjusted and software red filter was applied to shot without physical red filter.

Software red filter:

Physical red filter:

Histograms before monochrome conversion:

And here are some 100% details (physical filter on the left, software on the right):

I'm a bit confused about the sharpening-like effects of the physical red filter version and have triple cheked my settings, sharpening was 0 for both. Lower image is meant to illustrate the differences in local contrast.

The interpolation algorithms work absolutely fine when only 1 correctly exposed channel is available - otherwise they wouldn't be able to cope with objects that are purely one colour (red, green or blue).
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Matt GrumSep 27 '10 at 7:45

@Matt - sure, they work, but the question is if this is the best data to start out with.
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KarelSep 27 '10 at 7:50